release version 2.0.0

.dockerignore

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+.ipynb*
+.idea/*
+static/*
+tests/*
+data/tcga
+data/tcga.clinical.pkl
+data/tcga.genomic.pkl
+data/genes.csv
+data/genes.oncopanel.csv
+data/Final_gene_map_oncopanel.v1.txt
+dev_data/*
+elasticsearch/es_data/*
+dump/*
+*Dockerfile*
+.dockerignore
+**/.git
+**/.gitignore
+**/.gitattributes

.gitattributes

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+*.pkl filter=lfs diff=lfs merge=lfs -text

.gitignore

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+# ignore certs
+saml
+apache-*
+
+# ignore pycharm
+.idea/
+
+# ignore vscode
+.vscode/
+
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+env/
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+*.egg-info/
+.installed.cfg
+*.egg
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*,cover
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+target/
+
+# osx
+.DS_Store
+
+elasticsearch/es_data/*
+dump/*
+
+src/*
+python-xmlsec/*
+
+# mypy
+.mypy_cache
+dev_data/*

.gitlab-ci.yml

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+default:
+    image: python:3.7
+
+variables:
+    MONGO_HOST: "localhost"
+    MONGO_PORT: 27017
+    MONGO_USERNAME: ""
+    MONGO_PASSWORD: ""
+    MONGO_DBNAME: matchminer_test
+    MONGO_URI: mongodb://localhost:27017/matchminer_test
+    ONCOTREE_CUSTOM_DIR: /builds/matchminer/matchminerAPI/data/oncotree_file.txt
+    EMAIL_CONFIG: /builds/matchminer/matchminerAPI/email.config.json
+    SECRETS_JSON: /builds/matchminer/matchminerAPI/SECRETS_JSON.json
+
+before_script:
+    # install mongo
+    - apt-get update && apt install -y dirmngr gnupg apt-transport-https software-properties-common ca-certificates curl
+    - wget -qO - https://www.mongodb.org/static/pgp/server-4.2.asc | apt-key add -
+    - add-apt-repository 'deb https://repo.mongodb.org/apt/debian buster/mongodb-org/4.2 main'
+    - apt-get update
+    - apt-get install -y mongodb-org libxml2-dev libxslt1-dev libxmlsec1-dev
+    - DEBIAN_FRONTEND=noninteractive apt-get update --fix-missing && apt-get update
+    - mkdir -p /data/db && touch mongod.log
+    - mongod --logpath /builds/matchminer/matchminerAPI/mongod.log --quiet &
+
+    # load test data
+    - mongorestore -d matchminer_test --dir=tests/data
+    - pip install -r requirements.txt
+
+    # set secrets file and run tests
+    - echo "{\"MONGO_HOST\":\"$MONGO_HOST\",\"MONGO_PORT\":\"$MONGO_PORT\",\"MONGO_USERNAME\":\"$MONGO_USERNAME\",\"MONGO_PASSWORD\":\"$MONGO_PASSWORD\",\"MONGO_DBNAME\":\"$MONGO_DBNAME\",\"MONGO_URI\":\"$MONGO_URI\"}" > SECRETS_JSON.json
+
+run_test:
+  script:
+    - nosetests -v tests/unit
+    - nosetests -v --with-xunit --with-coverage tests
+
+
+  artifacts:
+    reports:
+      junit: nosetests.xml

Dockerfile

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+FROM python:3.8-slim
+
+# Install packages needed to compile dependencies:
+RUN DEBIAN_FRONTEND=noninteractive apt-get update --fix-missing && apt-get install -y \
+    libxml2-dev \
+    libxslt1-dev \
+    libxmlsec1-dev \
+    libxmlsec1-openssl \
+    pkg-config \
+    git \
+    gcc
+
+# Configure pip
+# Counterintuitively, PIP_NO_COMPILE=no is needed to turn compiling *off*
+# We do this partly because compiling is not reproducible, creating pointless diffs in images,
+# and partly to reduce image size.
+ENV PIP_NO_CACHE_DIR=1 PIP_NO_COMPILE=no
+RUN mkdir /matchminerAPI
+
+# Install requirements:
+COPY ./requirements.txt /matchminerAPI/requirements.txt
+WORKDIR /matchminerAPI
+RUN pip install -r requirements.txt
+
+# Hack to work around https://github.com/py-bson/bson/issues/82
+RUN pip --no-input uninstall --yes bson
+RUN pip --no-input uninstall --yes pymongo
+RUN pip install 'pymongo==3.10'
+
+ENV ONCOTREE_CUSTOM_DIR /matchminerAPI/data/oncotree_file.txt
+
+# Use an (anonymous) volume to hold "*.pyc" files:
+VOLUME /bytecode
+RUN mkdir -p /bytecode
+ENV PYTHONPYCACHEPREFIX=/bytecode
+
+# Expose and bind to port 80:
+EXPOSE 80
+CMD gunicorn wsgi:app --bind=0.0.0.0:80
+
+# Copy over source files:
+COPY . /matchminerAPI/

Dockerfile-dev

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+FROM python:3.7
+
+# install ubuntu packages.
+RUN DEBIAN_FRONTEND=noninteractive apt-get update --fix-missing && apt-get install -y \
+    libxml2-dev \
+    libxslt1-dev \
+    libxmlsec1-dev \
+ && apt-get clean \
+ && apt-get autoremove
+
+RUN mkdir /matchminerAPI
+COPY ./requirements.txt /matchminerAPI/requirements.txt
+WORKDIR /matchminerAPI
+
+RUN pip install -r requirements.txt
+
+# Hack to work around https://github.com/py-bson/bson/issues/82
+RUN pip --no-input uninstall --yes bson
+RUN pip --no-input uninstall --yes pymongo
+RUN pip install 'pymongo==3.10'

README.md

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+# MatchMiner API 
+Welcome to the documentation for the MatchMiner API! MatchMiner is a system designed to match cancer patients to genomically driven clinical trials using Clinical Trial Markup Language (CTML) and patient clinical and genomic data. 
+
+The MatchMiner platform can be used on local instances that provide access to private data. If you are interested in the development of new features, or in setting up a local instance of the MatchMiner system, please see the documentation, or contact [[email protected]](https://app.gitbook.com/@matchminer/s/matchminer)
+
+# [Documentation](https://matchminer.gitbook.io/)
+[Data Model](https://matchminer.gitbook.io/matchminer/matchminer-api/data-model)
+
+[Developer Setup](https://matchminer.gitbook.io/matchminer/matchminer-api/development-setup)

cerberus1/__init__.py

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+"""
+    Extensible validation for Python dictionaries.
+
+    :copyright: 2012-2016 by Nicola Iarocci.
+    :license: ISC, see LICENSE for more details.
+
+    Full documentation is available at http://python-cerberus.org/
+
+"""
+
+from .cerberus import Validator, DocumentError
+from .schema import rules_set_registry, schema_registry, Registry, SchemaError
+
+
+__version__ = "1.0rc"
+
+__all__ = [
+    DocumentError.__name__,
+    Registry.__name__,
+    SchemaError.__name__,
+    Validator.__name__,
+    'schema_registry',
+    'rules_set_registry'
+]